In e-books, footnotes don’t work well–so notes should be endnotes. This includes footnote-type remarks, references, etc etc.
We don’t much care how you format them, as long as there is *something* identifying each note in a way that can be searched and replaced. For example, bracketing the numbers with parentheses or brackets is OK, as long as those don’t occur elsewhere throughout the text.
More preferably, though, especially if you have many references, is to tag them. This may be done in Word, or with a specialized software such as EndNote. If you’re affiliated with an educational institution, it’s likely that EndNote will be available on your site license.
Any author who sends us an EndNote file along with the completed manuscript will receive a cookie–the yummy kind, too, not the software kind.
Always keep in mind: most of what we do involves search and replace. The easier this is for us to do, the quicker the formatting will go.